1
|
Yu X, Tang L, Tang X, Mao Y. Genome-Wide Identification and Analysis of MYB Transcription Factors in Pyropia yezoensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:3613. [PMID: 37896076 PMCID: PMC10609806 DOI: 10.3390/plants12203613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
MYB transcription factors are one of the largest transcription factor families in plants, and they regulate numerous biological processes. Red algae are an important taxonomic group and have important roles in economics and research. However, no comprehensive analysis of the MYB gene family in any red algae, including Pyropia yezoensis, has been conducted. To identify the MYB gene members of Py. yezoensis, and to investigate their family structural features and expression profile characteristics, a study was conducted. In this study, 3 R2R3-MYBs and 13 MYB-related members were identified in Py. yezoensis. Phylogenetic analysis indicated that most red algae MYB genes could be clustered with green plants or Glaucophyta MYB genes, inferring their ancient origins. Synteny analysis indicated that 13 and 5 PyMYB genes were orthologous to Pyropia haitanensis and Porphyra umbilicalis, respectively. Most Bangiaceae MYB genes contain several Gly-rich motifs, which may be the result of an adaptation to carbon limitations and maintenance of important regulatory functions. An expression profile analysis showed that PyMYB genes exhibited diverse expression profiles. However, the expression patterns of different members appeared to be diverse, and PyMYB5 was upregulated in response to dehydration, low temperature, and Pythium porphyrae infection. This is the first comprehensive study of the MYB gene family in Py. Yezoensis and it provides vital insights into the functional divergence of MYB genes.
Collapse
Affiliation(s)
- Xinzi Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lei Tang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xianghai Tang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yunxiang Mao
- MOE Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource & Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
2
|
Fiore M, Forli S, Manetti F. Targeting Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAPK2, MK2): Medicinal Chemistry Efforts To Lead Small Molecule Inhibitors to Clinical Trials. J Med Chem 2015; 59:3609-34. [PMID: 26502061 DOI: 10.1021/acs.jmedchem.5b01457] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The p38/MAPK-activated kinase 2 (MK2) pathway is involved in a series of pathological conditions (inflammation diseases and metastasis) and in the resistance mechanism to antitumor agents. None of the p38 inhibitors entered advanced clinical trials because of their unwanted systemic side effects. For this reason, MK2 was identified as an alternative target to block the pathway but avoiding the side effects of p38 inhibition. However, ATP-competitive MK2 inhibitors suffered from low solubility, poor cell permeability, and scarce kinase selectivity. Fortunately, non-ATP-competitive inhibitors of MK2 have been already discovered that allowed circumventing the selectivity issue. These compounds showed the additional advantage to be effective at lower concentrations in comparison to the ATP-competitive inhibitors. Therefore, although the significant difficulties encountered during the development of these inhibitors, MK2 is still considered as an attractive target to treat inflammation and related diseases to prevent tumor metastasis and to increase tumor sensitivity to chemotherapeutics.
Collapse
Affiliation(s)
- Mario Fiore
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Fabrizio Manetti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
| |
Collapse
|
3
|
Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med Chem 2014; 6:541-61. [PMID: 24649957 DOI: 10.4155/fmc.13.216] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are involved in many essential cellular processes and their deregulation can lead to a variety of diseases, including cancer. The pharmaceutical industry has invested heavily in the identification of kinase inhibitors to modulate these disease-promoting pathways, resulting in several successful drugs. However, the field is challenging as it is difficult to identify novel selective inhibitors with good pharmacokinetic/pharmacodynamic properties. In addition, resistance to kinase inhibitor treatment frequently arises. The identification of non-ATP site targeting ('allosteric') inhibitors, the identification of kinase activators and the expansion of kinase target space to include the less studied members of the family, including atypical- and pseudo-kinases, are potential avenues to overcome these challenges. In this perspective, the opportunities and challenges of following these approaches and others will be discussed.
Collapse
|
4
|
Fujino A, Fukushima K, Kubota T, Matsumoto Y, Takimoto-Kamimura M. Structure of the β-form of human MK2 in complex with the non-selective kinase inhibitor TEI-L03090. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1344-8. [PMID: 24316826 PMCID: PMC3855716 DOI: 10.1107/s1744309113030534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/07/2013] [Indexed: 06/02/2023]
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2), a serine/threonine kinase from the p38 mitogen-activated protein kinase signalling pathway, plays an important role in the production of TNF-α and other cytokines. In a previous report, it was shown that MK2 in complex with the selective inhibitor TEI-I01800 adopts an α-helical glycine-rich loop that is induced by the stable nonplanar conformer of TEI-I01800. To understand the mechanism of the structural change, the structure of MK2 bound to TEI-L03090, which lacks the key substituent found in TEI-I01800, was determined. MK2-TEI-L03090 has a β-sheet glycine-rich loop in common with other kinases, as predicted. This result suggests that a small compound can induce a drastic conformational change in the target protein structure and can be used to design potent and selective inhibitors.
Collapse
Affiliation(s)
- Aiko Fujino
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Kei Fukushima
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Takaharu Kubota
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Yoshiyuki Matsumoto
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| |
Collapse
|
5
|
Fujino A, Fukushima K, Kubota T, Kosugi T, Takimoto-Kamimura M. Crystal structure of human cyclin-dependent kinase-2 complex with MK2 inhibitor TEI-I01800: insight into the selectivity. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:905-9. [PMID: 24121337 PMCID: PMC3795553 DOI: 10.1107/s0909049513020736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 07/25/2013] [Indexed: 06/02/2023]
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the MK2-TEI-I01800 complex has been reported; its Gly-rich loop was found to form an α-helix, not a β-sheet as has been observed for other Ser/Thr kinases. TEI-I01800 is 177-fold selective against MK2 compared with CDK2; in order to understand the inhibitory mechanism of TEI-I01800, the cyclin-dependent kinase 2 (CDK2) complex structure with TEI-I01800 was determined at 2.0 Å resolution. Interestingly, the Gly-rich loop of CDK2 formed a β-sheet that was different from that of MK2. In MK2, TEI-I01800 changed the secondary structure of the Gly-rich loop from a β-sheet to an α-helix by collision between Leu70 and a p-ethoxyphenyl group at the 7-position and bound to MK2. However, for CDK2, TEI-I01800 bound to CDK2 without this structural change and lost the interaction with the substituent at the 7-position. In summary, the results of this study suggest that the reason for the selectivity of TEI-I01800 is the favourable conformation of TEI-I01800 itself, making it suitable for binding to the α-form MK2.
Collapse
Affiliation(s)
- Aiko Fujino
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Kei Fukushima
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Takaharu Kubota
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Tomomi Kosugi
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| |
Collapse
|
6
|
Pourbasheer E, Bazl R, Amanlou M. Molecular docking and 3D-QSAR studies on the MAPKAP-K2 inhibitors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0820-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
7
|
Wang TJ, Zhou L, Fei J, Li ZC, He LF. Applications of 3D-QSAR and structure-based pharmacophore modeling, virtual screening, ADMET, and molecular docking of putative MAPKAP-K2 (MK2) inhibitors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0492-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
8
|
EDMUNDS JEREMYJ, TALANIAN ROBERTV. MAPKAP Kinase 2 (MK2) as a Target for Anti-inflammatory Drug Discovery. ANTI-INFLAMMATORY DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735346-00158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Despite the success of anti-TNFα biologicals, there remains a significant unmet need for novel oral anti-inflammatory drugs for the treatment of rheumatoid arthritis and related diseases. Vigorous exploration of many potential targets for inhibition of, for example, pro-inflammatory cytokine production has led to efforts to find inhibitor leads targeting many enzymes including the p38α substrate kinase MK2. MK2 has a key role in the production of several pro-inflammatory cytokines, and studies with knockout animals and inhibitor leads support the promise of MK2 as an anti-inflammatory target. However, MK2 has additional biological roles such as in cell cycle checkpoint control, suggesting caution in the use of MK2 inhibitors for chronic non-life-threatening clinical indications such as inflammation. MK2 inhibitor lead identification and optimization efforts in several labs have resulted in a variety of potent and specific lead molecules, some of which display in-vivo activity. However, potency loss from enzyme to cell, and cell to in vivo, is commonly significant. Further, poor enzyme to cell potency correlations are also common for MK2 lead chemical series, suggesting uncontrolled confounding factors in lead inhibitor properties, or that the biological roles of MK2 and related enzymes may still be poorly understood. While further efforts in identification of MK2 inhibitors may yet yield viable drug leads, efforts to date suggest caution with this target.
Collapse
|